To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("BiSeq")

In most cases, you don't need to download the package archive at all.

BiSeq

Processing and analyzing bisulfite sequencing data

Bioconductor version: Release (3.0)

The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.

Author: Katja Hebestreit, Hans-Ulrich Klein

Maintainer: Katja Hebestreit <katjah at stanford.edu>

Citation (from within R, enter citation("BiSeq")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("BiSeq")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BiSeq")

 

PDF R Script An Introduction to BiSeq
PDF   Reference Manual

Details

biocViews DNAMethylation, Genetics, MethylSeq, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 2.12 (R-3.0)
License LGPL-3
Depends R (>= 2.15.2), methods, S4Vectors, IRanges(>= 1.17.24), GenomicRanges, Formula
Imports methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomicRanges, rtracklayer, parallel, betareg, lokern, Formula, globaltest
Suggests
System Requirements
URL
Depends On Me RRBSdata
Imports Me M3D
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source BiSeq_1.6.0.tar.gz
Windows Binary BiSeq_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) BiSeq_1.6.0.tgz
Mac OS X 10.9 (Mavericks) BiSeq_1.6.0.tgz
Browse/checkout source (username/password: readonly)
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